Question: Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
2
gravatar for memy
10 months ago by
memy20
memy20 wrote:

Hello there,

I am using Platanus-allee 2.2.2 to generate hybrid assembly of Illumina short reads and PacBio reads. I have got contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours

Error(13): Error, SolveDBG exception!! platanus_allee solve_DBG command failed.

Here is the script used for contig assembly and phasing

num_threads=20 
tmp_dir=/path-to-/tem/platanus_allee 
memory_GB=100 
out_prefix=out
minimap2_path=minimap2

# Input reads

PE=trimmed_L1_*.fq
PacBio=pacbio*.fastq.gz

# Contig assembly commands
platanus_allee assemble -t ${num_threads} -tmp ${tmp_dir} -m ${memory_GB} -o ${out_prefix} \
-f $PE \
2>${out_prefix}.assembleLog

# phasing commands 
platanus_allee phase -t ${num_threads} -tmp ${tmp_dir} -o ${out_prefix} -mapper ${minimap2_path} \
-c out_contig.fa \
-IP1 $PE -p $PacBio \ 
2>${out_prefix}.phaseLog

cat out.phaseLog

platanus_allee version: 2.2.2
platanus_allee phase -t 20 -tmp /path-to-/tem/platanus_allee -o out -mapper minimap2 -c out_contig.fa -IP1 trimmed_L1_1.fq trimmed_L1_2.fq -p /path-to-/pacbio*.fastq.gz 

Error(13): Error, SolveDBG exception!!
platanus_allee solve_DBG command failed.

tail -n 15 path-to-/out_intermediateResults/round1/out.solveDBGLog

dividing nodes based on bubbles ...
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 1832
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 0
TOTAL_NUM_DIVISIONS =1832

dividing erroneous scaffolds based on base-level coverages ...
Segmentation fault (core dumped)

A bug causing the segmentation fault seems issue on Platanus-allee v2.0.0 and earlier

Any suggestion please?

ADD COMMENTlink modified 10 months ago • written 10 months ago by memy20

I'm running into the same issue - platanus_allee assemble worked, but I get the error code when running the phasing command.

Did you end up finding a solution?

ADD REPLYlink written 7 days ago by jamesmalfieri0

Hi, I did not find a way to work it out and finally gave up on it and switched to my focus to SPAdes.

ADD REPLYlink written 6 days ago by memy20
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